Power conversion applications are becoming increasingly more sophisticated in having multiple sub-circuits that utilize multiple pulse width modulation (PWM) signal outputs that operate at different frequencies and are harmonically related to each other in frequency, i.e., integer frequency ratios. For example, one PWM signal frequency could be an integer multiple of another PWM signal frequency. Existing PWM generation technologies can generate these harmonically related PWM signal output frequencies, but since the counters in them are free running they are incapable of maintaining proper synchronization of the PWM signals in response to user configuration errors, update errors, phase offset changes, and/or in response to external asynchronous events such as an external synchronization signal that may cause an initial synchronization among the PWM signal outputs to be lost.